Our long-term goal is to advance the understanding, at the molecular level, of the pathogenicity and epidemiology of uropathogenic Escherichia coli (UPEC) strains to better target treatment and prophylaxis of urinary tract infections, reduce resistance, and provide information on possible targets for vaccines and antibiotics. The proposed studies are focused on understanding the basis of urovirulence of E. coli by the comparative genome-wide analysis of strains that will be isolated from a large number of patients with first-time and recurrent cystitis and healthy women. The central hypothesis is that the relatively few clonal groups involved in UPEC human pathogenesis can be defined and characterized as to their key genetic loci and the impact of genetic variations on UPEC virulence. Our preliminary data support that we can investigate sizeable samples of fresh isolates, establish strong clonal associations with recurrent cystitis and determine genome- wide the pathogenicity-adaptive genetic changes. We will determine how mutational changes (single nucleotide polymorphisms, small insertions/deletions, etc) and horizontal gene transfer contribute to the emergence of UPEC. Our aim is to potentially examine every gene shared by at least a portion of UPEC strains for being under positive selection for pathogenicity-adaptive mutations or horizontal transfer. For this, we will employ a population genomics-based analysis to trace the mutations and gene transfer, followed by assessment of the functional significance of the representative positively selected loci in UPEC.